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Affymetrix Subsidiary Perlegen Begins SNP Discovery Project

SAN FRANCISCO, March 5 - Affymetrix spin-off Perlegen has begun to generate data on 50 genomes, in the initial phase of its strategy to generate a wealth of SNP data that can be used to forge alliances with companies seeking to do genetic association studies, Affymetrix CEO Stephen Fodor told GenomeWeb

"The project has started; the train is leaving the station," Fodor said following his presentation at the Genome Tri Conference.

In an effort to support Perlegen, Affymetrix is developing ultra-high-density chips that will each contain 60 million probes -- compared with the 400,000 probes the company's chips have today. In effect, this would allow Perlegen to ask 60 million different questions per chip, Fodor said.

"One technician running three wafers a day is equal to 100 automated sequencers," said Fodor, adding that the company could generate 1,000 assays per second.

Once the data has been generated, Perlegen will seek to develop partnerships with companies in the pharmaceutical, cosmetics, and food industries, and other companies that have an interest in associating genetics with a particular outcome. Fodor did not say when he expected Perlegen to have enough data to enter the next phase or disclose the subject profiles Perlegen would focus on. 

The SNPs and haplotypes Perlegen finds will also be available to incorporate on Affymetrix chips. Fodor said it was too early to say whether the data would be available on the chips to allow for pattern matching, or for whole genome analysis.

Affymetrix is currently in the process of raising money for Perlegen, although Fodor would not elaborate on the details.

"It'll be announced when we finish raising money," Fodor said. Previously Affymetrix said that it hoped to raise about $100 million in third-party financing to support the venture, while maintaining a substantial equity position in Perlegen.

David Cox, formerly co-director of Stanford University's Genome Center, is leading Perlegen’s scientific efforts.

Meanwhile, Fodor also said that Neomorphic, the bioinformatics company Affy acquired in October, was busy improving the data in the public databases and developing ways to incorporate the data in useable formats. The new unit, known as Affymetrix Berkeley, will also build an Internet portal that connects information generated by the chips to the genome and vice versa.  

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